chr5-31927211-A-G

Variant names:

• chr5-31927211-A-G
• rs7719829
• NM_178140.4:c.477-55944A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_178140.4(PDZD2):​c.477-55944A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.594 in 151,920 control chromosomes in the GnomAD database, including 27,223 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.59 (27223 hom., cov: 32)
• Consequence: PDZD2 NM_178140.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

Genes affected

PDZD2 (HGNC:18486): (PDZ domain containing 2) The protein encoded by this gene contains six PDZ domains and shares sequence similarity with pro-interleukin-16 (pro-IL-16). Like pro-IL-16, the encoded protein localizes to the endoplasmic reticulum and is thought to be cleaved by a caspase to produce a secreted peptide containing two PDZ domains. In addition, this gene is upregulated in primary prostate tumors and may be involved in the early stages of prostate tumorigenesis. [provided by RefSeq, Dec 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDZD2	NM_178140.4	c.477-55944A>G		intron_variant	Intron 2 of 24	ENST00000438447.2	NP_835260.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDZD2	ENST00000438447.2	c.477-55944A>G		intron_variant	Intron 2 of 24	1	NM_178140.4	ENSP00000402033.1
PDZD2	ENST00000502489.5	n.233-55944A>G		intron_variant	Intron 1 of 17	2

Frequencies

GnomAD3 genomes AF: 0.594 AC: 90236 AN: 151802 Hom.: 27195 Cov.: 32

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.782

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.625

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.594 AC: 90300 AN: 151920 Hom.: 27223 Cov.: 32 AF XY: 0.596 AC XY: 44250 AN XY: 74232

Gnomad4 AFR AF: 0.510

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.782

Gnomad4 EAS AF: 0.781

Gnomad4 SAS AF: 0.578

Gnomad4 FIN AF: 0.650

Gnomad4 NFE AF: 0.610

Gnomad4 OTH AF: 0.628

Alfa AF: 0.612 Hom.: 37532

Bravo AF: 0.590

Asia WGS AF: 0.663 AC: 2303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.9
DANN	Benign	0.63

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7719829; hg19: chr5-31927317;